Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_083924362.1 D471_RS0128565 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000341125.1:WP_083924362.1 Length = 469 Score = 199 bits (506), Expect = 2e-55 Identities = 164/476 (34%), Positives = 222/476 (46%), Gaps = 43/476 (9%) Query: 17 SAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDTEL--GPLAGVPIA 74 +A + L R+ ++P++ A H+ E+A DARR D EL GPLAGVP+ Sbjct: 17 NAETVLREHLERVHALQPSLNAVA-----HLREKAALEDARRVDTDAELRDGPLAGVPVF 71 Query: 75 VKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMDEFAMGSSGESSA 134 VKD G+ T SR G+ FD+ V RL+ AGA+I+G M EF + +S +++ Sbjct: 72 VKDVHEVDGLPFTNGSRAFTGHTPDFDSEVAARLKRAGAVILGSTVMPEFGLRASTDNAL 131 Query: 135 FGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTGIVGLKPTYGY 194 G TRNPW+ E P GSS G+A AVAAG APLAL D GS R PAA G+VGLKPT G Sbjct: 132 HGTTRNPWNPEFGPAGSSGGAAVAVAAGLAPLALAGDGAGSGRLPAAACGVVGLKPTRGR 191 Query: 195 VSRYGVVAFA--SSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRTPPALKFGGEPS 252 V +G A+ + L PM R V D ARL +V++GP D TPP F G Sbjct: 192 VP-WGPSAYEHWAGLAISSPMARTVRDTARLLDVVSGPMTGDPYGLPATPPG-HFLGACD 249 Query: 253 LSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTEYALSAYYVIAVA 312 RL V L P RV + IA V + LP A+ Sbjct: 250 TQRERLRVAWTLTPP------HGRVHDDIADAVRSALDVFD-DLPH-----------ALV 291 Query: 313 EASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGTYVLSAGHYDAYY 372 EA+ +L A G L R + G + +A + A Sbjct: 292 EAAPDLGGMRDPLLAVMAGNVGALVRAVGPDRLDSVEAPSLEIARQGERMTAADYVAAVN 351 Query: 373 R-RAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGE-----KVDDPVSMYLGDIC-T 425 RA R L +E YD L+TPT +IGE + S Y D Sbjct: 352 ACRAGAARVL------GFWEEYDVLITPTATRPPLRIGEGPQGRSFAERWSFYADDFAFG 405 Query: 426 IPVNLAGLPAVSVPCGF-VDGLPVGMQLIGKPFADTQILQIAWAYQKVTKHHEARP 480 P N+ G PA+++PCG +G+PVGMQL+G+P A+ +L +A ++ + +P Sbjct: 406 YPFNMTGQPALTLPCGVDGNGVPVGMQLVGRPGAEDTLLGLAAQIERSPRTRRRKP 461 Lambda K H 0.318 0.135 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 668 Number of extensions: 46 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 488 Length of database: 469 Length adjustment: 34 Effective length of query: 454 Effective length of database: 435 Effective search space: 197490 Effective search space used: 197490 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory